Genetic analysis, including single nucleotide polymorphisms (SNPs) analysis, can provide a ground for so-called “tailor-made medicine”, and the necessity thereof is increasing rapidly. From the viewpoint of reducing side effects of drugs, the U.S. Food and Drug Administration is shifted to require SNPs information in relation to the effect of a new drug when the new drug application is submitted. In also Japan, the necessity of SNPs analysis is increasing rapidly.
In DNA chips which are presently widely used in SNPs analysis, the detection probes are synthetic DNA oligonucleotides. The DNA chips are mainly prepared by one of the following two methods. The first method is to immobilize separately synthesized DNA oligonucleotides on a surface of a substrate such as a slide glass (coupling synthesis method, refer to Non-Patent Document 1). The second method is to synthesize oligonucleotides on a substrate such as a slide glass (in-situ synthesis method, refer to Non-Patent Document 2).
In the coupling synthesis method, first, a highly reactive functional group is attached to a DNA oligonucleotide to give a DNA probe. Then, the given DNA probe is spotted on a surface of a substrate such as a slide glass, and thereby the probe molecule is immobilized on the substrate by a covalent bond formed by a chemical reaction between the DNA probe and a functional group present in the substrate surface. In this method, since the method of spotting DNA probe is complicated, it is very difficult to control efficiency of immobilization to a substrate surface, which also influences on the quality control.
In in-situ synthesis method, a probe is synthesized on a surface of a substrate such as a slide glass by optical lithography or bubble jetting. In this method, since DNA is synthesized at a specific position, the immobilization reaction of a DNA probe on a substrate surface can be omitted. Therefore, high-throughput synthesis of DNA chips is possible. However, in this in-situ synthesis method, the elongation efficiency of a DNA strand on a substrate surface is low, and the DNA probe purity is low. Thus, there is a disadvantage of low correctness. For example, DNA elongation efficiency in synthesis by optical lithography is about 95% at highest. For example, valid probe ratio of a 20-base probe is not higher than 40%. In other words, sequences of 60% or more probes are incorrect.
Non-Patent Document 1: Ange wandte Chemie international edition, 2002, 41, 1276-1289
Non-Patent Document 2: Biopolymer, 2004, 73, 579-596
The presence of a large number of probes having incorrect sequences causes a lack of accuracy in results of analyses, such as SNP analysis, which are required to be accurate and is a problem.
In conventional processes of preparing probes, it is necessary to bind a protecting group to a nucleotide base and removing this protecting group by ammonia treatment, lastly. However, the ammonia treatment cleaves the Si—O bond at an anchor portion, and thereby about 90% of DNA probes are detached from a support.
Therefore, it is an object of the present invention to provide an oligonucleotide derivative which can be used without occurrence of the above-mentioned problems when used in SNP, for example.
It is another object of the present invention to provide a method of utilizing the oligonucleotide derivative for detection of gene.